Myosinome: A Database of Myosins from Select Eukaryotic Genomes to Facilitate Analysis of Sequence-Structure-Function Relationships

Myosins are one of the largest protein superfamilies with 24 classes. They have conserved structural features and catalytic domains yet show huge variation at different domains resulting in a variety of functions. Myosins are molecules driving various kinds of cellular processes and motility until the level of organisms. These are ATPases that utilize the chemical energy released by ATP hydrolysis to bring about conformational changes leading to a motor function. Myosins are important as they are involved in almost all cellular activities ranging from cell division to transcriptional regulation. They are crucial due to their involvement in many congenital diseases symptomatized by muscular malfunctions, cardiac diseases, deafness, neural and immunological dysfunction, and so on, many of which lead to death at an early age. We present Myosinome, a database of selected myosin classes (myosin II, V, and VI) from five model organisms. This knowledge base provides the sequences, phylogenetic clustering, domain architectures of myosins and molecular models, structural analyses, and relevant literature of their coiled-coil domains. In the current version of Myosinome, information about 71 myosin sequences belonging to three myosin classes (myosin II, V, and VI) in five model organisms ( Homo Sapiens, Mus musculus, D. melanogaster, C. elegans and S. cereviseae) identified using bioinformatics surveys are presented, and several of them are yet to be functionally characterized. As these proteins are involved in congenital diseases, such a database would be useful in short-listing candidates for gene therapy and drug development. The database can be accessed from http://caps.ncbs.res.in/myosinome .

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Identification of high-efficiency 3′GG gRNA motifs in indexed FASTA files with ngg2

PeerJ Computer Science ◽

10.7717/peerj-cs.33 ◽

2015 ◽

Vol 1 ◽

pp. e33 ◽

Cited By ~ 2

Author(s):

Elisha D. Roberson

Keyword(s):

High Efficiency ◽

Homo Sapiens ◽

Model Organisms ◽

Proof Of Concept ◽

Protein Coding ◽

C Elegans ◽

Protein Coding Genes ◽

Starting Point ◽

Command Line Tool ◽

Reference Genomes

CRISPR/Cas9 is emerging as one of the most-used methods of genome modification in organisms ranging from bacteria to human cells. However, the efficiency of editing varies tremendously site-to-site. A recent report identified a novel motif, called the 3′GG motif, which substantially increases the efficiency of editing at all sites tested inC. elegans. Furthermore, they highlighted that previously published gRNAs with high editing efficiency also had this motif. I designed a Python command-line tool, ngg2, to identify 3′GG gRNA sites from indexed FASTA files. As a proof-of-concept, I screened for these motifs in six model genomes:Saccharomyces cerevisiae,Caenorhabditis elegans,Drosophila melanogaster,Danio rerio,Mus musculus, andHomo sapiens. I also scanned the genomes of pig (Sus scrofa) and African elephant (Loxodonta africana) to demonstrate the utility in non-model organisms. I identified more than 60 million single match 3′GG motifs in these genomes. Greater than 61% of all protein coding genes in the reference genomes had at least one unique 3′GG gRNA site overlapping an exon. In particular, more than 96% of mouse and 93% of human protein coding genes have at least one unique, overlapping 3′GG gRNA. These identified sites can be used as a starting point in gRNA selection, and the ngg2 tool provides an important ability to identify 3′GG editing sites in any species with an available genome sequence.

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Structural features and nucleotide-binding capability of the C subunit are integral to the regulation of the eukaryotic V1Vo ATPases

Biochemical Society Transactions ◽

10.1042/bst0330883 ◽

2005 ◽

Vol 33 (4) ◽

pp. 883-885 ◽

Cited By ~ 6

Author(s):

G. Grüber

Keyword(s):

Conformational Changes ◽

Atp Hydrolysis ◽

Structural Features ◽

Subunit C ◽

Reversible Dissociation ◽

Intracellular Compartments ◽

C Subunit ◽

Vacuolar Atpases ◽

Made In

V-ATPases (vacuolar ATPases) are responsible for acidification of intracellular compartments and, in certain cases, proton transport across the plasma membrane of eukaryotic cells. They are composed of a catalytic V1 sector, in which ATP hydrolysis takes place, and the Vo sector, which functions in proton conduction. The best established mechanism for regulating the V-ATPase activity in vivo involves reversible dissociation of the V1 and Vo domains, in which subunit C is intimately involved. In the last year, impressive progress has been made in elucidating the structure of the C subunit and its arrangement inside the V-ATPase. Nucleotide occupancy by subunit C, followed by conformational changes of this subunit has shed light on the mechanism of V-ATPase regulation.

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Domains of alpha-SNAP required for the stimulation of exocytosis and for N-ethylmalemide-sensitive fusion protein (NSF) binding and activation.

Molecular Biology of the Cell ◽

10.1091/mbc.7.5.693 ◽

1996 ◽

Vol 7 (5) ◽

pp. 693-701 ◽

Cited By ~ 40

Author(s):

R J Barnard ◽

A Morgan ◽

R D Burgoyne

Keyword(s):

Membrane Proteins ◽

Fusion Protein ◽

Conformational Changes ◽

Protein Interactions ◽

Atp Hydrolysis ◽

Coiled Coil ◽

Protein Protein Interactions ◽

Permeabilized Cells ◽

C Terminus ◽

Adrenal Chromaffin

The binding of alpha-SNAP to the membrane proteins syntaxin, SNAP-25, and synaptobrevin leads to the recruitment of the N-ethylmaleimide-sensitive fusion protein (NSF). ATP hydrolysis by NSF has been suggested to drive conformational changes in one or more of these membrane proteins that are essential for regulated exocytosis. Functional evidence for a role of alpha-SNAP in exocytosis in adrenal chromaffin cells comes from the ability of this protein to stimulate Ca(2+)-dependent exocytosis in digitonin-permeabilized cells. Here we examine the effect of a series of deletion mutants of alpha-SNAP on exocytosis, and on the ability of alpha-SNAP to interact with NSF, to define essential domains involved in protein-protein interactions in exocytosis. Deletion of extreme N- or C-terminal regions of alpha-SNAP produced proteins unable to bind to syntaxin or to stimulate exocytosis, suggesting that these domains participate in essential interactions. Deletion of C-terminal residues abolished the ability of alpha-SNAP to bind NSF. In contrast, deletion of up to 120 N-terminal residues did not prevent the binding of NSF to immobilized alpha-SNAP and such mutants were also able to stimulate the ATPase activity of NSF. These results suggest that the C-terminus, but not the N-terminus, of alpha-SNAP is crucial for interactions with NSF. The involvement of the C-terminus of alpha-SNAP, which contains a predicted coiled-coil domain, in the binding of both syntaxin and NSF would place the latter two proteins in proximity in a ternary complex whereupon the energy derived from ATP hydrolysis by NSF could induce a conformational change in syntaxin required for exocytosis to proceed.

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Myosin II isoforms in smooth muscle: heterogeneity and function

AJP Cell Physiology ◽

10.1152/ajpcell.00131.2007 ◽

2007 ◽

Vol 293 (2) ◽

pp. C493-C508 ◽

Cited By ~ 63

Author(s):

Thomas J. Eddinger ◽

Daniel P. Meer

Keyword(s):

Smooth Muscle ◽

Conformational Changes ◽

Atp Hydrolysis ◽

Expression Profiles ◽

Myosin Ii ◽

Thick Filament ◽

Actin Binding ◽

Head Region ◽

Organ Systems ◽

Species Specific

Both smooth muscle (SM) and nonmuscle class II myosin molecules are expressed in SM tissues comprising hollow organ systems. Individual SM cells may express one or more of multiple myosin II isoforms that differ in myosin heavy chain (MHC) and myosin light chain (MLC) subunits. Although much has been learned, the expression profiles, organization within contractile filaments, localization within cells, and precise roles in various contractile functions of these different myosin molecules are still not well understood. However, data supporting unique physiological roles for certain isoforms continues to build. Isoform differences located in the S1 head region of the MHC can alter actin binding and rates of ATP hydrolysis. Differences located in the MHC tail can alter the formation, stability, and size of the myosin thick filament. In these distinct ways, both head and tail isoform differences can alter force generation and muscle shortening velocities. The MLCs that are associated with the lever arm of the S1 head can affect the flexibility and range of motion of this domain and possibly the motion of the S2 and motor domains. Phosphorylation of MLC20 has been associated with conformational changes in the S1 and/or S2 fragments regulating enzymatic activity of the entire myosin molecule. A challenge for the future will be delineation of the physiological significance of the heterogeneous expression of these isoforms in developmental, tissue-specific, and species-specific patterns and or the intra- and intercellular heterogeneity of myosin isoform expression in SM cells of a given organ.

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Coupling of ATPase activity, microtubule binding and mechanics in the dynein motor domain

10.1101/309179 ◽

2018 ◽

Cited By ~ 1

Author(s):

Stefan Niekamp ◽

Nicolas Coudray ◽

Nan Zhang ◽

Ronald D. Vale ◽

Gira Bhabha

Keyword(s):

Atpase Activity ◽

Conformational Change ◽

Conformational Changes ◽

Large Scale ◽

Atp Hydrolysis ◽

Molecular Motor ◽

Coiled Coil ◽

Microtubule Binding ◽

Dynein Motor ◽

In The Wild

The movement of a molecular motor protein along a cytoskeletal track requires communication between enzymatic, polymer-binding, and mechanical elements. Such communication is particularly complex and not well understood in the dynein motor, an ATPase that is comprised of a ring of six AAA domains, a large mechanical element (linker) spanning over the ring, and a microtubule-binding domain (MTBD) that is separated from the AAA ring by a ~135 Å coiled-coil stalk. We identified mutations in the stalk that disrupt directional motion, have microtubule-independent hyperactive ATPase activity, and nucleotide-independent low affinity for microtubules. Cryo-electron microscopy structures of a mutant that uncouples ATPase activity from directional movement reveal that nucleotide-dependent conformational changes occur normally in one half of the AAA ring, but are disrupted in the other half. The large-scale linker conformational change observed in the wild-type protein is also inhibited, revealing that this conformational change is not required for ATP hydrolysis. These results demonstrate an essential role of the stalk in regulating motor activity and coupling conformational changes across the two halves of the AAA ring.

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Structural and Functional Insights on the Myosin Superfamily

Bioinformatics and Biology Insights ◽

10.4137/bbi.s8451 ◽

2012 ◽

Vol 6 ◽

pp. BBI.S8451 ◽

Cited By ~ 18

Author(s):

Divya P. Syamaladevi ◽

James A. Spudich ◽

R. Sowdhamini

Keyword(s):

Binding Site ◽

Conformational Changes ◽

Molecular Motors ◽

Weak Interactions ◽

Coiled Coil ◽

Actin Binding ◽

Model Organisms ◽

Physical Force ◽

Coiled Coil Domain ◽

Myosin Superfamily

The myosin superfamily is a versatile group of molecular motors involved in the transport of specific biomolecules, vesicles and organelles in eukaryotic cells. The processivity of myosins along an actin filament and transport of intracellular ‘cargo’ are achieved by generating physical force from chemical energy of ATP followed by appropriate conformational changes. The typical myosin has a head domain, which harbors an ATP binding site, an actin binding site, and a light-chain bound ‘lever arm’, followed often by a coiled coil domain and a cargo binding domain. Evolution of myosins started at the point of evolution of eukaryotes, S. cerevisiae being the simplest one known to contain these molecular motors. The coiled coil domain of the myosin classes II, V and VI in whole genomes of several model organisms display differences in the length and the strength of interactions at the coiled coil interface. Myosin II sequences have long-length coiled coil regions that are predicted to have a highly stable dimeric interface. These are interrupted, however, by regions that are predicted to be unstable, indicating possibilities of alternate conformations, associations to make thick filaments, and interactions with other molecules. Myosin V sequences retain intermittent regions of strong and weak interactions, whereas myosin VI sequences are relatively devoid of strong coiled coil motifs. Structural deviations at coiled coil regions could be important for carrying out normal biological function of these proteins.

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A library of coiled-coil domains: from regular bundles to peculiar twists

Bioinformatics ◽

10.1093/bioinformatics/btaa1041 ◽

2020 ◽

Author(s):

Krzysztof Szczepaniak ◽

Adriana Bukala ◽

Antonio Marinho da Silva Neto ◽

Jan Ludwiczak ◽

Stanislaw Dunin-Horkawicz

Keyword(s):

Protein Data Bank ◽

Conformational Changes ◽

Coiled Coil ◽

Data Bank ◽

Structural Features ◽

Coiled Coils ◽

Supplementary Information ◽

Numerical Representation ◽

Data Set ◽

Potential Applications

Abstract Motivation Coiled coils are widespread protein domains involved in diverse processes ranging from providing structural rigidity to the transduction of conformational changes. They comprise two or more α-helices that are wound around each other to form a regular supercoiled bundle. Owing to this regularity, coiled-coil structures can be described with parametric equations, thus enabling the numerical representation of their properties, such as the degree and handedness of supercoiling, rotational state of the helices, and the offset between them. These descriptors are invaluable in understanding the function of coiled coils and designing new structures of this type. The existing tools for such calculations require manual preparation of input and are therefore not suitable for the high-throughput analyses. Results To address this problem, we developed SamCC-Turbo, a software for fully-automated, per-residue measurement of coiled coils. By surveying Protein Data Bank with SamCC-Turbo, we generated a comprehensive atlas of ∼50,000 coiled-coil regions. This machine learning-ready data set features precise measurements as well as decomposes coiled-coil structures into fragments characterized by various degrees of supercoiling. The potential applications of SamCC-Turbo are exemplified by analyses in which we reveal general structural features of coiled coils involved in functions requiring conformational plasticity. Finally, we discuss further directions in the prediction and modeling of coiled coils. Availability SamCC-Turbo is available as a web server (https://lbs.cent.uw.edu.pl/samcc_turbo) and as a Python library (https://github.com/labstructbioinf/samcc_turbo), whereas the results of the Protein Data Bank scan can be browsed and downloaded at https://lbs.cent.uw.edu.pl/ccdb. Supplementary information Supplementary data are available at Bioinformatics online.

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Identification of high-efficiency 3’GG gRNA motifs in indexed FASTA files with ngg2

10.7287/peerj.preprints.969v2 ◽

2015 ◽

Author(s):

Elisha D Roberson

Keyword(s):

High Efficiency ◽

Homo Sapiens ◽

Model Organisms ◽

Proof Of Concept ◽

Protein Coding ◽

C Elegans ◽

Protein Coding Genes ◽

Starting Point ◽

Command Line Tool ◽

Reference Genomes

CRISPR/Cas9 is emerging as one of the most-used methods of genome modification in organisms ranging from bacteria to human cells. However, the efficiency of editing varies tremendously site-to-site. A recent report identified a novel motif, called the 3’GG motif, which substantially increases the efficiency of editing at all sites tested in C. elegans. Furthermore, they highlighted that previously published gRNAs with high editing efficiency also had this motif. I designed a python command-line tool, ngg2, to identify 3’GG gRNA sites from indexed FASTA files. As a proof-of-concept, I screened for these motifs in six model genomes: Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus, and Homo sapiens. I also scanned the genomes of pig (Sus scrofa) and African elephant (Loxodonta africana) to demonstrate the utility in non-model organisms. I identified more than 60 million single match 3’GG motifs in these genomes. Greater than 61% of all protein coding genes in the reference genomes had at least one unique 3’GG gRNA site overlapping an exon. In particular, more than 96% of mouse and 93% of human protein coding genes have at least one unique, overlapping 3’GG gRNA. These identified sites can be used as a starting point in gRNA selection, and the ngg2 tool provides an important ability to identify 3'GG editing sites in any species with an available genome sequence.

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Identification of high-efficiency 3’GG gRNA motifs in indexed FASTA files with ngg2

10.7287/peerj.preprints.969 ◽

2015 ◽

Author(s):

Elisha D Roberson

Keyword(s):

High Efficiency ◽

Homo Sapiens ◽

Model Organisms ◽

Proof Of Concept ◽

Protein Coding ◽

C Elegans ◽

Protein Coding Genes ◽

Starting Point ◽

Command Line Tool ◽

Reference Genomes

CRISPR/Cas9 is emerging as one of the most-used methods of genome modification in organisms ranging from bacteria to human cells. However, the efficiency of editing varies tremendously site-to-site. A recent report identified a novel motif, called the 3’GG motif, which substantially increases the efficiency of editing at all sites tested in C. elegans. Furthermore, they highlighted that previously published gRNAs with high editing efficiency also had this motif. I designed a python command-line tool, ngg2, to identify 3’GG gRNA sites from indexed FASTA files. As a proof-of-concept, I screened for these motifs in six model genomes: Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus, and Homo sapiens. I also scanned the genomes of pig (Sus scrofa) and African elephant (Loxodonta africana) to demonstrate the utility in non-model organisms. I identified more than 60 million single match 3’GG motifs in these genomes. Greater than 61% of all protein coding genes in the reference genomes had at least one unique 3’GG gRNA site overlapping an exon. In particular, more than 96% of mouse and 93% of human protein coding genes have at least one unique, overlapping 3’GG gRNA. These identified sites can be used as a starting point in gRNA selection, and the ngg2 tool provides an important ability to identify 3'GG editing sites in any species with an available genome sequence.

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Sulfurous Gases As Biological Messengers and Toxins: Comparative Genetics of Their Metabolism in Model Organisms

Journal of Toxicology ◽

10.1155/2011/394970 ◽

2011 ◽

Vol 2011 ◽

pp. 1-14 ◽

Cited By ~ 26

Author(s):

Neal D. Mathew ◽

David I. Schlipalius ◽

Paul R. Ebert

Keyword(s):

Homo Sapiens ◽

Biological Activities ◽

Model Organisms ◽

Homologous Proteins ◽

C Elegans ◽

Signalling Molecules ◽

Reducing Conditions ◽

Mercaptopyruvate Sulfurtransferase ◽

Sulfurous Compounds ◽

Sulfur Containing

Gasotransmitters are biologically produced gaseous signalling molecules. As gases with potent biological activities, they are toxic as air pollutants, and the sulfurous compounds are used as fumigants. Most investigations focus on medical aspects of gasotransmitter biology rather than toxicity toward invertebrate pests of agriculture. In fact, the pathways for the metabolism of sulfur containing gases in lower organisms have not yet been described. To address this deficit, we use protein sequences fromHomo sapiensto query Genbank for homologous proteins inCaenorhabditis elegans,Drosophila melanogaster, andSaccharomyces cerevisiae. InC. elegans, we find genes for all mammalian pathways for synthesis and catabolism of the three sulfur containing gasotransmitters, H2S, SO2and COS. The genes for H2S synthesis have actually increased in number inC. elegans. Interestingly,D. melanogasterand Arthropoda in general, lack a gene for 3-mercaptopyruvate sulfurtransferase, an enzym for H2S synthesis under reducing conditions.

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